[Dock-fans] de novo drug design

Dong Xu d1xu at ucsd.edu
Wed Jul 16 18:48:19 PDT 2008

Hi John,

Thanks for all the info! I will check them out. For Cactvs, is this the
right link?



On Wed, Jul 16, 2008 at 12:10 PM, John J. Irwin <jji at cgl.ucsf.edu> wrote:

> Hi DX
> I don't know of any free de novo design tools. I do know about Allegrow
> http://bostondenovo.com/ and Sprout http://www.simbiosys.ca/, but have no
> idea about price.
> For scaffold hopping, try ROCS/EON from OpenEye (http://eyesopen.com/)
> which is a shape approach, and is free to accredited academics. OE also have
> a tool for directly mutating one atom at a time, BROOD, but it may be a
> challenge to test some of those suggestions experimentally.  Cactvs is free
> to academics and incorporates fingerprint methods that can be use to
> essentially scaffold hop (find similar molecules).  molinspiration.com is
> free to academics and has a tool to break up molecules into fragments, which
> is a useful underlying technology for scaffold hopping.
> Of course, none of these programs works directly with DOCK - I interpreted
> your "can be used along with" liberally.
> John
> Dong Xu wrote:
>> Hi Dock fans,
>> Are there are freely available de novo drug design tools that can be used
>> along with Dock? I'm interested in tools that do core/scaffold hopping and
>> pharmacophore.
>> Thanks!
>> -DX
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